pycom02g25840

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
pyrus_communis
Chr2
OG0000258
Physical Location & Seq
Reverse (-)
23734100 .. 23735109
1010 bp
Loading structure...
UTR
Exon/CDS
Intron
pycom02g25840.1

Sequence Viewer

Length: 858 bp
ATGAGTGGCACCAAGTGTGTTGTCAAACAAGTTGAAGAATTCCAAGTGCTTGTTCATGAGTTAGATGAAGAAAATCTTGGTCTGAAAGAAGGTTTTGTGGTTGGCTCTATTATAAAGAAATTGCCTTCGAATTGGAAAGGCTTTAAGGTTTATCTGAAGCATTTAACTGAAGACATAAGCATGGATCAATTGATTCTCAAACTGTTTGTGGAGGAGGATCATCACAAAAATGAGAAGTATGATGTCTCATCGCTGGAGGCAAAAACCAATGTTGTGGAAGGAGGTGACTCACACAAGACAGGTCATAGGGCAAATGATTGCCGCCACAAGAAGGATCAGAATTCTAGGAGTTCTAATGAAGCAAACGTTGCAGAGGACACGTTTGTTGCTGTTATATCTAAAGTCAATTTATTGACCAATTCCAATGACTGGTGGGTTGATACAGGAGCAACAAGGCATGTGTGTGCTGATTGGAATTTATTTGTTACTTACCAATCCATTGATGGTGGAGAAAATCTGTACATGGGGAATGCAACAGCATCTGCTGTTGCAGAGAAGGGAAAATTGACGCTCAAACTTACTTTTGGAAAAGAGCTTTCACTCACCAATGTTCTACATGTTCTTGATATTCGCAAGAATATGATTTTTAGTTCGCTTTTGAGTAACAAAGGTTTCAAAATAGTCTTTGAATATGATAAGTTTGTAATCACCAAGGGTGGGGTGTATGTGGGAAAGGGCTACCTGGCTGAAGGGCTCTTCAAACTGAATGTACTTTCTGCTAACGTTATTAATAATAATTACAAGCCTAATGCTTCTTCTGCTTACTTGATTGAGTCTTCTACATTATGGCATGGTTAA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
No ontology terms assigned.
KEGG Pathways
Metabolic & Signaling
No pathways identified.
Pfam Domains
Protein Families
Retrotran_gag_2

Protein Analysis

286

Amino Acids

31.84

Weight (kDa)

6.56

Isoelectric Point (pI)

25.11

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 1 - 79 4.7e-08 gag-polypeptide of LTR copia-type
Pol_BBD PF22936 144 - 225 1e-18 Pol polyprotein, beta-barrel domain
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Publication-ready
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Orthologous Genes (Group: OG0000258)

Species Orthologous Gene IDs
arabidopsis_thaliana AT4G00980
fragaria_vesca FvH4_1g25682 FvH4_2g13961 FvH4_2g20162 FvH4_2g24753 FvH4_3g12191 FvH4_3g12632 FvH4_3g16171 FvH4_4g05871 FvH4_4g05873 FvH4_4g10121 FvH4_4g15488 FvH4_4g23911 FvH4_4g27782 FvH4_5g08912 FvH4_5g23001 FvH4_5g24552 FvH4_5g32801 FvH4_5g32802 FvH4_6g05093 FvH4_6g19722 FvH4_6g20391 FvH4_6g33792 FvH4_7g01381 FvH4_7g16761 FvH4_7g16761 FvH4_7g16761
malus_domestica MD01G1082500.v1.1 MD15G1436400.v1.1
prunus_persica Prupe.2G021400_v2.0.a1 Prupe.2G052400_v2.0.a1 Prupe.2G065000_v2.0.a1 Prupe.2G187700_v2.0.a1 Prupe.2G187800_v2.0.a1 Prupe.2G189900_v2.0.a1 Prupe.2G191300_v2.0.a1 Prupe.2G191700_v2.0.a1 Prupe.4G265600_v2.0.a1 Prupe.7G014200_v2.0.a1 Prupe.7G039000_v2.0.a1
pyrus_communis pycom01g05590 pycom01g05910 pycom02g12230 pycom02g25840 pycom03g15580 pycom04g04480 pycom05g09230 pycom05g23350 pycom05g23360 pycom07g08380 pycom09g01980 pycom09g01990 pycom11g18190 pycom11g18200 pycom11g21580 pycom13g04160 pycom15g25800 pycom16g16210 pycom16g17230 pycom16g24560 pycom16g25700 pycom17g11020
rosa_chinensis RchiOBHm_Chr1g0359981 RchiOBHm_Chr2g0151961 RchiOBHm_Chr2g0171331 RchiOBHm_Chr5g0081471 RchiOBHm_Chr6g0283031 RchiOBHm_Chr7g0197111 RchiOBHm_Chr7g0222601
rosa_laevigata RLG00000027843 RLG00000027845 RLG00000030065
rosa_multiflora Rmu_sc0000381.1_g000031 Rmu_sc0001179.1_g000035 Rmu_sc0001616.1_g000046 Rmu_sc0001851.1_g000032 Rmu_sc0002152.1_g000013 Rmu_sc0004031.1_g000015 Rmu_sc0004645.1_g000003 Rmu_sc0007393.1_g000001 Rmu_sc0008949.1_g000003 Rmu_sc0009799.1_g000011 Rmu_sc0011614.1_g000001 Rmu_sc0011699.1_g000009 Rmu_sc0019280.1_g000001 Rmu_sc0023984.1_g000001 Rmu_ssc0000050.1_g000036
rosa_roxburghii Rroxscaffold_1G00022650 Rroxscaffold_1G00033480 Rroxscaffold_3G00270250 Rroxscaffold_4G00296600 Rroxscaffold_4G00296760 Rroxscaffold_6G00409840
rosa_rugosa Rorug01G0273800 Rorug01G0273900 Rorug01G0274000
rosa_samantha Rh1AG287300 Rh1AG288100 Rh1BG253000 Rh1BG253500 Rh1BG399800 Rh1CG270400 Rh1CG271000 Rh1DG282000 Rh1DG282500 Rh4DG126500 Rh5DG194600 Rh5DG461100
rosa_wichuraiana Rw0G009130 Rw1G002590 Rw1G008490 Rw1G012210 Rw1G014290 Rw1G014490 Rw1G025510 Rw2G025840 Rw2G026170 Rw2G036510 Rw3G003050 Rw4G009270 Rw5G002350 Rw5G013930 Rw5G019500 Rw5G025890 Rw5G029960 Rw5G032360 Rw6G009890 Rw6G015670 Rw6G015860 Rw7G010030 Rw7G032600 Rw7G032770

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AanI TTATAA 1 cut(s) 113
AccB1I GGYRCC 1 cut(s) 8
AccB7I CCANNNNNTGG 1 cut(s) 429
AciI CCGC 1 cut(s) 322
AclI AACGTT 2 cut(s) 366, 783
AclWI GGATC 3 cut(s) 192, 225, 342
AcsI RAATTY 3 cut(s) 38, 340, 475
AcuI CTGAAG 3 cut(s) 176, 189, 768
AdeI CACNNNGTG 1 cut(s) 15
AfaI GTAC 2 cut(s) 521, 771
AfiI CCNNNNNNNGG 3 cut(s) 331, 429, 717
AflIII ACRYGT 2 cut(s) 378, 616
AgsI TTSAA 4 cut(s) 35, 676, 689, 760
AjnI CCWGG 1 cut(s) 741
AjuI GAANNNNNNNTTGG 4 cut(s) 36, 60, 68, 92
AluBI AGCT 1 cut(s) 595
AluI AGCT 1 cut(s) 595
Alw26I GTCTC 1 cut(s) 250
AlwI GGATC 3 cut(s) 192, 225, 342
AlwNI CAGNNNCTG 1 cut(s) 542
ApoI RAATTY 3 cut(s) 38, 340, 475
AseI ATTAAT 1 cut(s) 789
AsuHPI GGTGA 3 cut(s) 296, 595, 700
AsuII TTCGAA 1 cut(s) 128
BanI GGYRCC 1 cut(s) 8
BanII GRGCYC 1 cut(s) 756
BbsI GAAGAC 2 cut(s) 177, 828
BccI CCATC 1 cut(s) 497
BciT130I CCWGG 1 cut(s) 743
BcoDI GTCTC 1 cut(s) 250
BfaI CTAG 1 cut(s) 345
BisI GCNGC 1 cut(s) 322
BlsI GCNGC 1 cut(s) 323
Bme1390I CCNGG 1 cut(s) 743
BmiI GGNNCC 1 cut(s) 10
BmrFI CCNGG 1 cut(s) 743
BmsI GCATC 1 cut(s) 548
BpiI GAAGAC 2 cut(s) 177, 828
BpmI CTGGAG 1 cut(s) 275
Bpu14I TTCGAA 1 cut(s) 128
BsaJI CCNNGG 1 cut(s) 711
Bsc4I CCNNNNNNNGG 3 cut(s) 331, 429, 717
Bse1I ACTGG 1 cut(s) 434
BseBI CCWGG 1 cut(s) 743
BseDI CCNNGG 1 cut(s) 711
BseLI CCNNNNNNNGG 3 cut(s) 331, 429, 717
BseNI ACTGG 1 cut(s) 434
BseRI GAGGAG 1 cut(s) 227
BshNI GGYRCC 1 cut(s) 8
BslI CCNNNNNNNGG 3 cut(s) 331, 429, 717
BsmAI GTCTC 1 cut(s) 250
BsmI GAATGC 1 cut(s) 535
Bsp119I TTCGAA 1 cut(s) 128
Bsp1286I GDGCHC 1 cut(s) 756
Bsp1407I TGTACA 1 cut(s) 519
Bsp143I GATC 3 cut(s) 184, 217, 334
BspACI CCGC 1 cut(s) 322
BspHI TCATGA 1 cut(s) 55
BspLI GGNNCC 1 cut(s) 10
BspPI GGATC 3 cut(s) 192, 225, 342
BspQI GCTCTTC 1 cut(s) 761
BspT104I TTCGAA 1 cut(s) 128
BspT107I GGYRCC 1 cut(s) 8
BsrGI TGTACA 1 cut(s) 519
BsrI ACTGG 1 cut(s) 434
BssECI CCNNGG 1 cut(s) 711
BssMI GATC 3 cut(s) 184, 217, 334
BssT1I CCWWGG 1 cut(s) 711
Bst2UI CCWGG 1 cut(s) 743
Bst4CI ACNGT 1 cut(s) 204
Bst6I CTCTTC 1 cut(s) 761
BstAPI GCANNNNNTGC 1 cut(s) 368
BstAUI TGTACA 1 cut(s) 519
BstBI TTCGAA 1 cut(s) 128
BstKTI GATC 3 cut(s) 187, 220, 337
BstMAI GTCTC 1 cut(s) 250
BstMBI GATC 3 cut(s) 184, 217, 334
BstMWI GCNNNNNNNGC 2 cut(s) 368, 818
BstNI CCWGG 1 cut(s) 743
BstNSI RCATGY 2 cut(s) 461, 620
BstSCI CCNGG 1 cut(s) 741
BstV2I GAAGAC 2 cut(s) 177, 828
BstXI CCANNNNNNTGG 1 cut(s) 274
BtgZI GCGATG 1 cut(s) 234
CaiI CAGNNNCTG 1 cut(s) 542
CciI TCATGA 1 cut(s) 55
CseI GACGC 1 cut(s) 577
Csp6I GTAC 2 cut(s) 520, 770
CviAII CATG 6 cut(s) 56, 181, 458, 523, 617, 851
CviJI RGCY 7 cut(s) 105, 141, 595, 738, 746, 754, 805
CviKI_1 RGCY 7 cut(s) 105, 141, 595, 738, 746, 754, 805
CviQI GTAC 2 cut(s) 520, 770
DpnI GATC 3 cut(s) 186, 219, 336
DpnII GATC 3 cut(s) 184, 217, 334
DraIII CACNNNGTG 1 cut(s) 15
Eam1104I CTCTTC 1 cut(s) 761
EarI CTCTTC 1 cut(s) 761
Eco130I CCWWGG 1 cut(s) 711
Eco24I GRGCYC 1 cut(s) 756
Eco57I CTGAAG 3 cut(s) 176, 189, 768
EcoRI GAATTC 2 cut(s) 38, 340
EcoRII CCWGG 1 cut(s) 741
EcoT14I CCWWGG 1 cut(s) 711
EcoT38I GRGCYC 1 cut(s) 756
ErhI CCWWGG 1 cut(s) 711
FaeI CATG 6 cut(s) 59, 184, 461, 526, 620, 854
FalI AAGNNNNNCTT 2 cut(s) 60, 92
FatI CATG 6 cut(s) 55, 180, 457, 522, 616, 850
Fnu4HI GCNGC 1 cut(s) 322
FriOI GRGCYC 1 cut(s) 756
Fsp4HI GCNGC 1 cut(s) 322
FspBI CTAG 1 cut(s) 345
GluI GCNGC 1 cut(s) 322
GsuI CTGGAG 1 cut(s) 275
HgaI GACGC 1 cut(s) 577
Hin1II CATG 6 cut(s) 59, 184, 461, 526, 620, 854
HinfI GANTC 3 cut(s) 193, 287, 833
HphI GGTGA 3 cut(s) 296, 595, 700
Hpy188I TCNGA 3 cut(s) 84, 156, 339
Hpy188III TCNNGA 2 cut(s) 56, 623
HpyAV CCTTC 6 cut(s) 83, 135, 272, 325, 550, 743
HpyCH4III ACNGT 1 cut(s) 204
HpyCH4IV ACGT 3 cut(s) 366, 380, 783
HpyCH4V TGCA 3 cut(s) 371, 533, 551
HpyF10VI GCNNNNNNNGC 2 cut(s) 368, 818
HpySE526I ACGT 3 cut(s) 366, 380, 783
Hsp92II CATG 6 cut(s) 59, 184, 461, 526, 620, 854
Kzo9I GATC 3 cut(s) 184, 217, 334
LguI GCTCTTC 1 cut(s) 761
LmnI GCTCC 1 cut(s) 446
LpnPI CCDG 6 cut(s) 239, 285, 415, 429, 728, 755
LweI GCATC 1 cut(s) 548
MaeI CTAG 1 cut(s) 345
MaeII ACGT 3 cut(s) 366, 380, 783
MaeIII GTNAC 3 cut(s) 284, 484, 662
MalI GATC 3 cut(s) 186, 219, 336
MboI GATC 3 cut(s) 184, 217, 334
MboII GAAGA 6 cut(s) 47, 80, 182, 748, 807, 828
MfeI CAATTG 1 cut(s) 188
MhlI GDGCHC 1 cut(s) 756
MlyI GAGTC 2 cut(s) 281, 842
MnlI CCTC 5 cut(s) 205, 208, 250, 275, 367
MseI TTAA 4 cut(s) 144, 164, 789, 856
MslI CAYNNNNRTG 3 cut(s) 179, 228, 462
MspR9I CCNGG 1 cut(s) 743
MunI CAATTG 1 cut(s) 188
Mva1269I GAATGC 1 cut(s) 535
MvaI CCWGG 1 cut(s) 743
MwoI GCNNNNNNNGC 2 cut(s) 368, 818
NdeII GATC 3 cut(s) 184, 217, 334
NlaIII CATG 6 cut(s) 59, 184, 461, 526, 620, 854
NlaIV GGNNCC 1 cut(s) 10
NmuCI GTSAC 1 cut(s) 284
NspI RCATGY 2 cut(s) 461, 620
NspV TTCGAA 1 cut(s) 128
PagI TCATGA 1 cut(s) 55
PciI ACATGT 1 cut(s) 616
PciSI GCTCTTC 1 cut(s) 761
PctI GAATGC 1 cut(s) 535
PfeI GAWTC 1 cut(s) 193
PflMI CCANNNNNTGG 1 cut(s) 429
PkrI GCNGC 1 cut(s) 323
PleI GAGTC 2 cut(s) 281, 841
PpsI GAGTC 2 cut(s) 281, 841
PscI ACATGT 1 cut(s) 616
PshBI ATTAAT 1 cut(s) 789
PsiI TTATAA 1 cut(s) 113
Psp1406I AACGTT 2 cut(s) 366, 783
Psp6I CCWGG 1 cut(s) 741
PspGI CCWGG 1 cut(s) 741
PspN4I GGNNCC 1 cut(s) 10
PstNI CAGNNNCTG 1 cut(s) 542
RsaI GTAC 2 cut(s) 521, 771
RsaNI GTAC 2 cut(s) 520, 770
RseI CAYNNNNRTG 3 cut(s) 179, 228, 462
SapI GCTCTTC 1 cut(s) 761
SaqAI TTAA 4 cut(s) 144, 164, 789, 856
SatI GCNGC 1 cut(s) 322
Sau3AI GATC 3 cut(s) 184, 217, 334
SchI GAGTC 2 cut(s) 281, 842
ScrFI CCNGG 1 cut(s) 743
SduI GDGCHC 1 cut(s) 756
SfaNI GCATC 1 cut(s) 548
SfuI TTCGAA 1 cut(s) 128
SmiMI CAYNNNNRTG 3 cut(s) 179, 228, 462
SsiI CCGC 1 cut(s) 322
SspMI CTAG 1 cut(s) 345
StyD4I CCNGG 1 cut(s) 741
StyI CCWWGG 1 cut(s) 711
TaaI ACNGT 1 cut(s) 204
TaiI ACGT 3 cut(s) 369, 383, 786
TaqI TCGA 1 cut(s) 128
TatI WGTACW 2 cut(s) 519, 769
TauI GCSGC 1 cut(s) 324
TfiI GAWTC 1 cut(s) 193
Tru1I TTAA 4 cut(s) 144, 164, 789, 856
Tru9I TTAA 4 cut(s) 144, 164, 789, 856
TseFI GTSAC 1 cut(s) 284
Tsp45I GTSAC 1 cut(s) 284
TspDTI ATGAA 3 cut(s) 44, 81, 372
Van91I CCANNNNNTGG 1 cut(s) 429
VspI ATTAAT 1 cut(s) 789
XapI RAATTY 3 cut(s) 38, 340, 475
XceI RCATGY 2 cut(s) 461, 620
XcmI CCANNNNNNNNNTGG 1 cut(s) 500
XspI CTAG 1 cut(s) 345
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.